Using a logical model to predict the growth of yeast

<p>Abstract</p> <p>Background</p> <p>A logical model of the known metabolic processes in <it>S. cerevisiae </it>was constructed from iFF708, an existing Flux Balance Analysis (FBA) model, and augmented with information from the KEGG online pathway database. The use of predicate logic as the knowledge representation for modelling enables an explicit representation of the structure of the metabolic network, and enables logical inference techniques to be used for model identification/improvement.</p> <p>Results</p> <p>Compared to the FBA model, the logical model has information on an additional 263 putative genes and 247 additional reactions. The correctness of this model was evaluated by comparison with iND750 (an updated FBA model closely related to iFF708) by evaluating the performance of both models on predicting empirical minimal medium growth data/essential gene listings.</p> <p>Conclusion</p> <p>ROC analysis and other statistical studies revealed that use of the simpler logical form and larger coverage results in no significant degradation of performance compared to iND750.</p

Facial features of patients with sickle cell anemia

Objective: To characterize the craniofacial features of patients with sickle cell anemia (SCA). Materials and Methods: Fifty patients with SCA in the north of Minas Gerais, Brazil, were evaluated using standardized photographs (front and profile) for a subjective facial analysis and digital radiographs for a computerized cephalometric analysis. To obtain linear and angular measurements, cephalometric points were marked on the digital images by a single examiner, using the program Radiocef 6.0, and facial analyses were performed by four different orthodontists. Results: Of the population studied, 28 patients were female with a mean age of 27.7 years. Most of the patients (64%) had their faces classified as esthetically acceptable, although results showed a predominance of convex profiles (72%). The mean of the SNA angle was 84.56 degrees, diagnosing proper positioning of the maxilla from the base of the skull. The prevalence of pattern II was 32%, and 31% showed maxillary protrusion; the effective length of the maxilla was reduced in 64%. Retrusion of the mandible was observed in 30%, and 76% had reduced mandibular length. Four measurements (mandibular length, maxillary length, anterior face height, and maxillomandibular difference) showed statistically significant differences between genders, where these measurements were higher for males than for females. Conclusion: Most patients did not show compensatory maxillary expansion, which was determined by the prevalence of decreased maxillary length (64%) and by the absence of maxillary protrusion in 69% of the SCA patients evaluated. (Angle Orthod. 2011;81:115-120.)811115120Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG

Challenges of Ageing in Portugal: Data from the EpiDoC Cohort

Introduction: Portuguese adults have a long lifespan, but it is unclear whether they live a healthy life in their final years. We aimed to determine the prevalence of multimorbidity and characterize lifestyle and other health outcomes among older Portuguese adults. Material and Methods: We performed a cross-sectional evaluation of 2393 adults, aged 65 and older, during the second wave of follow-up of the EpiDoC cohort, a population-based study involving long-term follow-up of a representative sample of the Portuguese population. Subjects completed a structured questionnaire during a telephone interview. Socioeconomic, demographic, lifestyle behaviours, chronic diseases, and health resources consumption were assessed. Cluster analysis was done to identify dietary patterns. Descriptive and analytic analysis was performed to estimate multimorbidity prevalence and its associated factors. Results: Multimorbidity prevalence among older adults was 78.3%, increased with age strata (72.8% for 65 - 69 years to 83.4% for >= 80 years), and was highest in Azores (84.9%) and Alentejo (83.6%). The most common chronic diseases were hypertension (57.3%), rheumatic disease (51.9%), hypercholesterolemia (49.4%), and diabetes (22.7%). Depression symptoms were frequent (11.8%) and highest in the oldest strata. The mean health-related quality of life (EQ-5D-3L) score was 0.59 +/- 0.38. Hospitalization in the previous 12 months was reported by 25.8% of individuals. Overall, 66.6% of older adults were physically inactive. 'Fruit and vegetables dietary pattern' was followed by 85.4% of individuals; however, regional inequalities were found (69% in Azores). Obesity prevalence was 22.3% overall and was highest among Azoreans (33%). Conclusion: The high prevalence of multimorbidity, combined with unhealthy lifestyle behaviours, suggests that the elderly population constitutes a vulnerable group warranting dedicated intervention

Advancing Tests of Relativistic Gravity via Laser Ranging to Phobos

Phobos Laser Ranging (PLR) is a concept for a space mission designed to advance tests of relativistic gravity in the solar system. PLR's primary objective is to measure the curvature of space around the Sun, represented by the Eddington parameter $\gamma$, with an accuracy of two parts in $10^7$, thereby improving today's best result by two orders of magnitude. Other mission goals include measurements of the time-rate-of-change of the gravitational constant, $G$ and of the gravitational inverse square law at 1.5 AU distances--with up to two orders-of-magnitude improvement for each. The science parameters will be estimated using laser ranging measurements of the distance between an Earth station and an active laser transponder on Phobos capable of reaching mm-level range resolution. A transponder on Phobos sending 0.25 mJ, 10 ps pulses at 1 kHz, and receiving asynchronous 1 kHz pulses from earth via a 12 cm aperture will permit links that even at maximum range will exceed a photon per second. A total measurement precision of 50 ps demands a few hundred photons to average to 1 mm (3.3 ps) range precision. Existing satellite laser ranging (SLR) facilities--with appropriate augmentation--may be able to participate in PLR. Since Phobos' orbital period is about 8 hours, each observatory is guaranteed visibility of the Phobos instrument every Earth day. Given the current technology readiness level, PLR could be started in 2011 for launch in 2016 for 3 years of science operations. We discuss the PLR's science objectives, instrument, and mission design. We also present the details of science simulations performed to support the mission's primary objectives.Comment: 25 pages, 10 figures, 9 table

Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models

In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. What differentiates this approach is the integration of an orthogonal-based local identifiability method into the unscented Kalman filter (UKF), rather than using the more common observability-based method which has inherent limitations. It also introduces a variable step size based on the system uncertainty of the UKF during the sensitivity calculation. This method identified 10 out of 12 parameters as identifiable. These ten parameters were estimated using the UKF, which was run 97 times. Throughout the repetitions the UKF proved to be more consistent than the estimation algorithms used for comparison

Degradation studies of hydrophilic, partially degradable and bioactive cements (HDBCs) incorporating chemically modified starch

The degradation rate in Hydrophilic, Degradable and Bioactive Cements (HDBCs) containing starch/cellulose acetate blends (SCA) is still low. In order to increase degradation, higher amounts of starch are required to exceed the percolation threshold. In this work, gelatinization, acetylation and methacrylation of corn starch were performed and assessed as candidates to replace SCA in HDBCs. Formulations containing methacrylated starch were prepared with different molar ratios of 2-hydroxyethyl methacrylate and methyl methacrylate in the liquid component and the amount of residual monomer released into water was evaluated. The concentration of reducing sugars, percentage of weight loss and morphologic analyses after degradation all confirmed increased degradation of HDBC with alpha-amylase, with the appearance of pores and voids from enzymatic action. Methacrylated starch therefore is a better alternative to be used as the solid component of HDBC then SCA, since it leads to the formation of cements with a lower release of toxic monomers and more prone to hydrolytic degradation while keeping the other advantages of HDBCs.The authors acknowledge to Foundation for Science and Technology (FCT), who supported this study through funds from project Concept2Cement (POCTI/CTM/60735/2004)

Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns.

The neural mechanisms determining the timing of even simple actions, such as when to walk or rest, are largely mysterious. One intriguing, but untested, hypothesis posits a role for ongoing activity fluctuations in neurons of central action selection circuits that drive animal behavior from moment to moment. To examine how fluctuating activity can contribute to action timing, we paired high-resolution measurements of freely walking Drosophila melanogaster with data-driven neural network modeling and dynamical systems analysis. We generated fluctuation-driven network models whose outputs-locomotor bouts-matched those measured from sensory-deprived Drosophila. From these models, we identified those that could also reproduce a second, unrelated dataset: the complex time-course of odor-evoked walking for genetically diverse Drosophila strains. Dynamical models that best reproduced both Drosophila basal and odor-evoked locomotor patterns exhibited specific characteristics. First, ongoing fluctuations were required. In a stochastic resonance-like manner, these fluctuations allowed neural activity to escape stable equilibria and to exceed a threshold for locomotion. Second, odor-induced shifts of equilibria in these models caused a depression in locomotor frequency following olfactory stimulation. Our models predict that activity fluctuations in action selection circuits cause behavioral output to more closely match sensory drive and may therefore enhance navigation in complex sensory environments. Together these data reveal how simple neural dynamics, when coupled with activity fluctuations, can give rise to complex patterns of animal behavior